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Footprinting at low temperatures: evidence that ethidium and other simple intercalators can discriminate between different nucleotide sequences.

Authors
  • Fox, K R
  • Waring, M J
Type
Published Article
Journal
Nucleic acids research
Publication Date
Jan 26, 1987
Volume
15
Issue
2
Pages
491–507
Identifiers
PMID: 3822813
Source
Medline
License
Unknown

Abstract

Footprinting experiments employing DNAase I have been performed at 4 degrees C. At this temperature several simple intercalating ligands, including both ethidium and proflavine, can be seen to induce marked changes in the pattern of cleavage. From an analysis of the changes in patterns of digestion by DNAase I we deduce that ethidium binds best to regions of mixed nucleotide sequence, especially those containing alternating purines and pyrimidines. Binding seems to be weakest to poly dA sequences which consequently appear as regions of relatively enhanced cleavage. Attempts to reproduce these changes using DNAase II as a footprinting tool were unsuccessful.

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